diff mask_image.xml @ 3:ca1421f7e3ed draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"

--- a/mask_image.xml	Thu Apr 16 05:45:02 2020 -0400
+++ b/mask_image.xml	Mon May 11 07:57:09 2020 -0400
@@ -6,7 +6,7 @@
     </macros>
 
     <expand macro="py_requirements"/>
-    <expand macro="cmd_modules" />
+    <expand macro="cmd_modules" /> 
 
     <configfiles>
         <inputs name="inputs"/>
@@ -52,45 +52,62 @@
     new_count = module_count + 1
     lines[4] = k + ":%d\n" % new_count
 
-    with open("output", "w") as f:
+    with open("output.cppipe", "w") as f:
         f.writelines(lines)
         f.write(writemi())
 
-f.close()
-        </configfile>    
+    f.close()
+        </configfile>
     </configfiles>
 
     <inputs>
 
-        <expand macro="input_pipeline_macro" />
-        <param name="input_image" label="Select input image" type="text">
+        <expand macro="input_pipeline_param" />
+        <param name="input_image" label="Enter the name of the input image" type="text">
             <expand macro="text_validator" />
         </param>
 
-        <param name="name_output_image" type="text" label="Name the output image">
+        <param name="name_output_image" type="text" label="Enter the name of the resulting image">
             <expand macro="text_validator" />
         </param>
 
         <conditional name="con_img_obj">
             <param name="img_obj" label="Use objects or an image as a mask?" type="select">
+                <help>
+                    <![CDATA[
+                        You can mask an image in two ways:
+                        <br> - Objects: Using objects created by another module (for instance IdentifyPrimaryObjects).
+                        The module will mask out all parts of the image that are not within one of the objects (unless you invert the mask).
+                        <br> - Image: Using a binary image as the mask, where black portions of the image (false or zero-value pixels) will be masked out.
+                        If the image is not binary, the module will use all pixels whose intensity is greater than 0.5 as the mask’s foreground (white area).
+                        You can use Threshold instead to create a binary image with finer control over the intensity choice.
+                        ]]>
+                </help>
                 <option value="Objects">Objects</option>
                 <option value="Image">Image</option>
             </param>
-           <when value="Objects">
-               <param name="select_obj" label="Select object for mask" type="text"/>
-           </when>
-           <when value="Image">
-               <param name="select_img" label="Select image for mask" type="text"/>
-           </when>
+            <when value="Objects">
+                <param name="select_obj" label="Enter the name objects to mask the input image" type="text"/>
+            </when>
+            <when value="Image">
+                <param name="select_img" label="Select image for mask" type="text"/>
+            </when>
         </conditional>
         <param name="invert_mask" label="Invert the mask?" type="select" display="radio">
+            <help>
+                <![CDATA[
+                    This option reverses the foreground/background relationship of the mask.
+                    <br> - Select "No" to produce the mask from the foreground (white portion) of the masking image or the area within the masking objects.
+                    <br> - Select "Yes" to instead produce the mask from the background (black portions) of the masking image or the area outside the masking objects.
+                    ]]>
+            </help>
             <option value="Yes">Yes</option>
             <option value="No">No</option>
         </param>
     </inputs>
 
     <outputs>
-        <expand macro="output_pipeline_macro" />
+        <expand macro="output_pipeline_param" />
     </outputs>
 
     <tests>
@@ -103,11 +120,27 @@
                 <param name="select_obj" value="Nuclei" />
             </conditional>
             <param name="invert_mask" value="No" />
-            <expand macro="test_out_file" file="mask_image.txt" />
+            <expand macro="test_out_file" file="mask_image.cppipe" />
         </test>
     </tests>
 
-    <expand macro="help" module="GrayToColor" />
+    <help>
+        <![CDATA[
+            .. class:: infomark
+
+            **What it does**
+
+            This tool masks an image so you can use the mask downstream in the pipeline.
+            The masked image is based on the original image and the masking object or image that is selected.
+            If using a masking image, the mask is composed of the foreground (white portions);
+            if using a masking object, the mask is composed of the area within the object.
+            Note that the image created by this tool for further processing downstream is grayscale.
+            If a binary mask is desired in subsequent tools, use the Threshold tool instead of MaskImage.
+
+            @COMMON_HELP@
+            ]]>
+    </help>
+
     <expand macro="citations" />
 
 </tool>